enabling a research data management beyond data heterogeneity

A primary goal of a research infrastructure for data management should be to enable efficient data discovery and integration of heterogeneous data. The German Federation for Biological Data (GFBio) was envisioned by this goal. The basic component, that enables such interoperability and serves as a backbone for such a platform, is the GFBio Terminology Service (GFBio TS). It acts as a semantic platform for accessing, developing and reasoning over terminological resources within the biological and environmental domain. A RESTful API gives access to these terminological resources in a uniform way regardless of their degree of complexity and whether they are internally stored or externally accessed through their web services. Additionally, a set of widgets with an intrinsic API connection are made available for an easy integration in applications and web interfaces. Based on the requirements of the GFBio partners, we describe the added value that is provided by the GFBio Terminology Service with practical scenarios but also, what challenges we still face. We conclude by describing our current activities and future developments

Nanosized aerosols from consumer sprays: experimental analysis and exposure modeling for four commercial products

Consumer spray products are already on the market in the cosmetics and household sector, which suggest by their label that they contain engineered nanoparticles (ENP). Sprays are considered critical for human health, because the lungs represent a major route for the uptake of ENP into the human body. To contribute to the exposure assessment of ENP in consumer spray products, we analyzed ENP in four commercially available sprays: one antiperspirant, two shoe impregnation sprays, and one plant-strengthening agent. The spray dispersions were analyzed by inductively coupled plasma mass spectrometry (ICPMS) and (scanning-) transmission electron microscopy ((S)TEM). Aerosols were generated by using the original vessels, and analyzed by scanning mobility particle sizer (SMPS) and (S)TEM. On the basis of SMPS results, the nanosized aerosol depositing in the respiratory tract was modeled for female and male consumers. The derived exposure levels reflect a single spray application. We identified ENP in the dispersions of two products (shoe impregnation and plant spray). Nanosized aerosols were observed in three products that contained propellant gas. The aerosol number concentration increased linearly with the sprayed amount, with the highest concentration resulting from the antiperspirant. Modeled aerosol exposure levels were in the range of 1010 nanosized aerosol components per person and application event for the antiperspirant and the impregnation sprays, with the largest fraction of nanosized aerosol depositing in the alveolar region. Negligible exposure from the application of the plant spray (pump spray) was observe

Size-fractionated characterization and quantification of nanoparticle release rates from a consumer spray product containing engineered nanoparticles

This study describes methods developed for reliable quantification of size- and element-specific release of engineered nanoparticles (ENP) from consumer spray products. A modified glove box setup was designed to allow controlled spray experiments in a particle-minimized environment. Time dependence of the particle size distribution in a size range of 10-500nm and ENP release rates were studied using a scanning mobility particle sizer (SMPS). In parallel, the aerosol was transferred to a size-calibrated electrostatic TEM sampler. The deposited particles were investigated using electron microscopy techniques in combination with image processing software. This approach enables the chemical and morphological characterization as well as quantification of released nanoparticles from a spray product. The differentiation of solid ENP from the released nano-sized droplets was achieved by applying a thermo-desorbing unit. After optimization, the setup was applied to investigate different spray situations using both pump and gas propellant spray dispensers for a commercially available water-based nano-silver spray. The pump spray situation showed no measurable nanoparticle release, whereas in the case of the gas spray, a significant release was observed. From the results it can be assumed that the homogeneously distributed ENP from the original dispersion grow in size and change morphology during and after the spray process but still exist as nanometer particles of size <100nm. Furthermore, it seems that the release of ENP correlates with the generated aerosol droplet size distribution produced by the spray vessel type used. This is the first study presenting results concerning the release of ENP from spray product

Size-fractionated characterization and quantification of nanoparticle release rates from a consumer spray product containing engineered nanoparticles

This study describes methods developed for reliable quantification of size- and element-specific release of engineered nanoparticles (ENP) from consumer spray products. A modified glove box setup was designed to allow controlled spray experiments in a particle-minimized environment. Time dependence of the particle size distribution in a size range of 10-500 nm and ENP release rates were studied using a scanning mobility particle sizer (SMPS). In parallel, the aerosol was transferred to a size-calibrated electrostatic TEM sampler. The deposited particles were investigated using electron microscopy techniques in combination with image processing software. This approach enables the chemical and morphological characterization as well as quantification of released nanoparticles from a spray product. The differentiation of solid ENP from the released nano-sized droplets was achieved by applying a thermo-desorbing unit. After optimization, the setup was applied to investigate different spray situations using both pump and gas propellant spray dispensers for a commercially available water-based nano-silver spray. The pump spray situation showed no measurable nanoparticle release, whereas in the case of the gas spray, a significant release was observed. From the results it can be assumed that the homogeneously distributed ENP from the original dispersion grow in size and change morphology during and after the spray process but still exist as nanometer particles of size < 100 nm. Furthermore, it seems that the release of ENP correlates with the generated aerosol droplet size distribution produced by the spray vessel type used. This is the first study presenting results concerning the release of ENP from spray products

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma

Burkitt lymphoma (BL) is the most common B-cell lymphoma in children. Within the International Cancer Genome Consortium (ICGC), we performed whole genome and transcriptome sequencing of 39 sporadic BL. Here, we unravel interaction of structural, mutational, and transcriptional changes, which contribute to MYC oncogene dysregulation together with the pathognomonic IG-MYC translocation. Moreover, by mapping IGH translocation breakpoints, we provide evidence that the precursor of at least a subset of BL is a B-cell poised to express IGHA. We describe the landscape of mutations, structural variants, and mutational processes, and identified a series of driver genes in the pathogenesis of BL, which can be targeted by various mechanisms, including IG-non MYC translocations, germline and somatic mutations, fusion transcripts, and alternative splicing

Bupropion for the treatment of apathy in Huntington's disease:A multicenter, randomised, double-blind, placebo-controlled, prospective crossover trial

OBJECTIVE:To evaluate the efficacy and safety of bupropion in the treatment of apathy in Huntington's disease (HD). METHODS:In this phase 2b multicentre, double-blind, placebo-controlled crossover trial, individuals with HD and clinical signs of apathy according to the Structured Clinical Interview for Apathy-Dementia (SCIA-D), but not depression (n = 40) were randomized to receive either bupropion 150/300mg or placebo daily for 10 weeks. The primary outcome parameter was a significant change of the Apathy Evaluation Scale (AES) score after ten weeks of treatment as judged by an informant (AES-I) living in close proximity with the study participant. The secondary outcome parameters included changes of 1. AES scores determined by the patient (AES-S) or the clinical investigator (AES-C), 2. psychiatric symptoms (NPI, HADS-SIS, UHDRS-Behavior), 3. cognitive performance (SDMT, Stroop, VFT, MMSE), 4. motor symptoms (UHDRS-Motor), 5. activities of daily function (TFC, UHDRS-Function), and 6. caregiver distress (NPI-D). In addition, we investigated the effect of bupropion on brain structure as well as brain responses and functional connectivity during reward processing in a gambling task using magnetic resonance imaging (MRI). RESULTS:At baseline, there were no significant treatment group differences in the clinical primary and secondary outcome parameters. At endpoint, there was no statistically significant difference between treatment groups for all clinical primary and secondary outcome variables. Study participation, irrespective of the intervention, lessened symptoms of apathy according to the informant and the clinical investigator. CONCLUSION:Bupropion does not alleviate apathy in HD. However, study participation/placebo effects were observed, which document the need for carefully controlled trials when investigating therapeutic interventions for the neuropsychiatric symptoms of HD. TRIAL REGISTRATION:ClinicalTrials.gov 01914965

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma

Burkitt lymphoma (BL) is the most common B-cell lymphoma in children. Within the International Cancer Genome Consortium (ICGC), we performed whole genome and transcriptome sequencing of 39 sporadic BL. Here, we unravel interaction of structural, mutational, and transcriptional changes, which contribute to MYC oncogene dysregulation together with the pathognomonic IG-MYC translocation. Moreover, by mapping IGH translocation breakpoints, we provide evidence that the precursor of at least a subset of BL is a B-cell poised to express IGHA. We describe the landscape of mutations, structural variants, and mutational processes, and identified a series of driver genes in the pathogenesis of BL, which can be targeted by various mechanisms, including IG-non MYC translocations, germline and somatic mutations, fusion transcripts, and alternative splicing

Rheumatoid arthritis - treatment: 180. Utility of Body Weight Classified Low-Dose Leflunomide in Japanese Rheumatoid Arthritis

Background: In Japan, more than 20 rheumatoid arthritis (RA) patients died of interstitial pneumonia (IP) caused by leflunomide (LEF) were reported, but many of them were considered as the victims of opportunistic infection currently. In this paper, efficacy and safety of low-dose LEF classified by body weight (BW) were studied. Methods: Fifty-nine RA patients were started to administrate LEF from July 2007 to July 2009. Among them, 25 patients were excluded because of the combination with tacrolimus, and medication modification within 3 months before LEF. Remaining 34 RA patients administered 20 to 50 mg/week of LEF were followed up for 1 year and enrolled in this study. Dose of LEF was classified by BW (50 mg/week for over 50 kg, 40 mg/week for 40 to 50 kg and 20 to 30 mg/week for under 40 kg). The average age and RA duration of enrolled patients were 55.5 years old and 10.2 years. Prednisolone (PSL), methotrexate (MTX) and etanercept were used in 23, 28 and 2 patients, respectively. In case of insufficient response or adverse effect, dosage change or discontinuance of LEF were considered. Failure was defined as dosages up of PSL and MTX, or dosages down or discontinuance of LEF. Last observation carried forward method was used for the evaluation of failed patients at 1 year. Results: At 1 year after LEF start, good/ moderate/ no response assessed by the European League Against Rheumatism (EULAR) response criteria using Disease Activity Score, including a 28-joint count (DAS28)-C reactive protein (CRP) were showed in 14/ 10/ 10 patients, respectively. The dosage changes of LEF at 1 year were dosage up: 10, same dosage: 5, dosage down: 8 and discontinuance: 11 patients. The survival rate of patients in this study was 23.5% (24 patients failed) but actual LEF continuous rate was 67.6% (11 patients discontinued) at 1 year. The major reason of failure was liver dysfunction, and pneumocystis pneumonia was occurred in 1 patient resulted in full recovery. One patient died of sepsis caused by decubitus ulcer infection. DAS28-CRP score was decreased from 3.9 to 2.7 significantly. Although CRP was decreased from 1.50 to 0.93 mg/dl, it wasn't significant. Matrix metalloproteinase (MMP)-3 was decreased from 220.0 to 174.2 ng/ml significantly. Glutamate pyruvate transaminase (GPT) was increased from 19 to 35 U/l and number of leukocyte was decreased from 7832 to 6271 significantly. DAS28-CRP, CRP, and MMP-3 were improved significantly with MTX, although they weren't without MTX. Increase of GPT and leukopenia were seen significantly with MTX, although they weren't without MTX. Conclusions: It was reported that the risks of IP caused by LEF in Japanese RA patients were past IP history, loading dose administration and low BW. Addition of low-dose LEF is a potent safe alternative for the patients showing unsatisfactory response to current medicines, but need to pay attention for liver function and infection caused by leukopenia, especially with MTX. Disclosure statement: The authors have declared no conflicts of interes

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements